rs80355771

Variant names:

• chr6-11714661-GA-G
• rs80355771
• NM_032744.4:c.659-150delT

Your query was ambiguous. Multiple possible variants found:

• chr6-11714661-GA-G
• chr6-11714661-GA-GAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_032744.4(ADTRP):​c.659-150delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000144 in 693,462 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 0 publications found

Genes affected

ADTRP (HGNC:21214): (androgen dependent TFPI regulating protein) Enables hydrolase activity. Involved in several processes, including cell migration involved in sprouting angiogenesis; negative regulation of secretion by cell; and positive regulation of macromolecule metabolic process. Located in caveola and cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADTRP	NM_032744.4	c.659-150delT		intron_variant	Intron 5 of 5	ENST00000414691.8	NP_116133.1
ADTRP	NM_001143948.2	c.713-150delT		intron_variant	Intron 6 of 6		NP_001137420.1
ADTRP	XM_011514956.2	c.765-150delT		intron_variant	Intron 6 of 6		XP_011513258.1
ADTRP	XM_047419420.1	c.378-150delT		intron_variant	Intron 6 of 6		XP_047275376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8	c.659-150delT		intron_variant	Intron 5 of 5	1	NM_032744.4	ENSP00000404416.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000144 AC: 1 AN: 693462 Hom.: 0 AF XY: 0.00000280 AC XY: 1 AN XY: 357238

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000629 AC: 1 AN: 15904

American (AMR) AF: 0.00 AC: 0 AN: 19180

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15598

East Asian (EAS) AF: 0.00 AC: 0 AN: 30746

South Asian (SAS) AF: 0.00 AC: 0 AN: 47950

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3780

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 481120

Other (OTH) AF: 0.00 AC: 0 AN: 33594

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs80355771; hg19: chr6-11714894;